Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
A searchable table of the S. cerevisiae pangenome ORFs defined in Peter et al. (2018) Nature (LINK) is provided below. The listed core/accessory classification and origin assignment are based on the original study. Click on the PanORF ID to find out the detailed presence/absence pattern of the corresponding pangenome ORF in both ScRAPdb and the 1002ScGP strain collections (which were recalculated by ScRAPdb).
| PanORF ID | SGD systematic Name | SGD standard name | Alias | Description | Type | Origin assignment | Mostly likely origin species | NCBI megablast hit |
|---|---|---|---|---|---|---|---|---|
| 2063-YBR082C | YBR082C | UBC4 | E2 ubiquitin-conjugating protein UBC4 | Ubiquitin-conjugating enzyme (E2); key E2 partner with Ubc1p for the anaphase-promoting complex (APC); mediates degradation of abnormal or excess proteins, including calmodulin and histone H3; regulates levels of DNA Polymerase-{alpha} to promote efficient and accurate DNA replication; interacts with many SCF ubiquitin protein ligases; component of the cellular stress response; UBC4 has a paralog, UBC5, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2064-YBR083W | YBR083W | TEC1 | ROC1 | Transcription factor targeting filamentation genes and Ty1 expression; Ste12p activation of most filamentation gene promoters depends on Tec1p and Tec1p transcriptional activity is dependent on its association with Ste12p; binds to TCS elements upstream of filamentation genes, which are regulated by Tec1p/Ste12p/Dig1p complex; competes with Dig2p for binding to Ste12p/Dig1p; positive regulator of chronological life span; TEA/ATTS DNA-binding domain family member | Core | NA | NA | NA |
| 2065-YBR084C-A | YBR084C-A | RPL19A | eL19|ribosomal 60S subunit protein L19A|L19e|rpl5L|YL14|L23A|L19A | Ribosomal 60S subunit protein L19A; rpl19a and rpl19b single null mutations result in slow growth, while the double null mutation is lethal; homologous to mammalian ribosomal protein L19, no bacterial homolog; RPL19A has a paralog, RPL19B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2066-YBR084W | YBR084W | MIS1 | trifunctional formate-tetrahydrofolate ligase/methenyltetrahydrofolate cyclohydrolase/methylenetetrahydrofolate dehydrogenase MIS1 | Mitochondrial C1-tetrahydrofolate synthase; involved in interconversion between different oxidation states of tetrahydrofolate (THF); provides activities of formyl-THF synthetase, methenyl-THF cyclohydrolase, and methylene-THF dehydrogenase | Core | NA | NA | NA |
| 2067-YBR085C-A | YBR085C-A | NA | NA | Protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and to the nucleus; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 2068-YBR085W | YBR085W | AAC3 | ADP/ATP carrier protein AAC3|ANC3 | Mitochondrial inner membrane ADP/ATP translocator; exchanges cytosolic ADP for mitochondrially synthesized ATP; expressed under anaerobic conditions; similar to Aac1p; has roles in maintenance of viability and in respiration; AAC3 has a paralog, PET9, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2069-YBR086C | YBR086C | IST2 | NA | Cortical ER protein involved in ER-plasma membrane tethering; one of 6 proteins (Ist2p, Scs2p, Scs22p, Tcb1p, Tcb2p, Tcb3p) that connect ER to the plasma membrane (PM) and regulate PM phosphatidylinositol-4-phosphate (PI4P) levels by controlling access of Sac1p phosphatase to its substrate PI4P in the PM; localizes to the mother cell in small-budded cells and to the bud in medium- and large-budded cells; mRNA is transported to the bud tip by an actomyosin-driven process | Core | NA | NA | NA |
| 2070-YBR087W | YBR087W | RFC5 | replication factor C subunit 5 | Subunit of heteropentameric Replication factor C (RF-C); RF-C is a DNA binding protein and ATPase that acts as a clamp loader of the proliferating cell nuclear antigen (PCNA) processivity factor for DNA polymerases delta and epsilon | Core | NA | NA | NA |
| 2071-YBR088C_NumOfGenes_2 | YBR088C | POL30 | proliferating cell nuclear antigen|PCNA | Proliferating cell nuclear antigen (PCNA); functions as the sliding replication clamp for DNA polymerase delta; may function as a docking site for other proteins required for mitotic and meiotic chromosomal DNA replication and for DNA repair; PCNA ubiquitination at K164 plays a crucial role during Okazaki fragment processing | Core | NA | NA | NA |
| 2072-YBR089C-A | YBR089C-A | NHP6B | high-mobility group nucleosome-binding protein|YBR090C-A | High-mobility group (HMG) protein; binds to and remodels nucleosomes; involved in recruiting FACT and other chromatin remodelling complexes to the chromosomes; functionally redundant with Nhp6Ap; required for transcriptional initiation fidelity of some tRNA genes; homologous to mammalian HMGB1 and HMGB2; NHP6B has a paralog, NHP6A, that arose from the whole genome duplication | Core | NA | NA | NA |
| 2073-YBR090C | YBR090C | NA | NA | Putative protein of unknown function; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm and nucleus | Core | NA | NA | NA |
| 2074-YBR091C_NumOfGenes_2 | YBR091C | TIM12 | MRS5 | Essential protein of the inner mitochondrial membrane; peripherally localized; component of the TIM22 complex, which is a twin-pore translocase that mediates insertion of numerous multispanning inner membrane proteins | Core | NA | NA | NA |
| 2075-YBR092C | YBR092C | PHO3 | acid phosphatase PHO3|phoC | Constitutively expressed acid phosphatase similar to Pho5p; brought to the cell surface by transport vesicles; hydrolyzes thiamin phosphates in the periplasmic space, increasing cellular thiamin uptake; expression is repressed by thiamin | Accessory | Ancestral | NA | NA |
| 2076-YBR093C | YBR093C | PHO5 | acid phosphatase PHO5|phoE | Repressible acid phosphatase; 1 of 3 repressible acid phosphatases that also mediates extracellular nucleotide-derived phosphate hydrolysis; secretory pathway derived cell surface glycoprotein; induced by phosphate starvation and coordinately regulated by PHO4 and PHO2 | Accessory | Ancestral | NA | NA |
| 2077-YBR094W | YBR094W | PBY1 | putative tubulin tyrosine ligase | Putative tubulin tyrosine ligase associated with P-bodies; may have a role in mRNA metabolism; yeast knockout collection strain identified as a pby1 null mutant is actually wild-type for PBY1 and deleted for mms4 | Core | NA | NA | NA |